• using R Under development (unstable) (2026-07-13 r90246)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)     GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-07-14 00:17:55 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘PoolTestR/DESCRIPTION’ ... OK
• this is package ‘PoolTestR’ version ‘0.2.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
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• checking whether package ‘PoolTestR’ can be installed ... [322s/333s] OK See the install log for details.
• used C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
• checking C++ specification ... INFO   specified C++17
• checking package directory ... OK
• checking DESCRIPTION meta-information ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘getPrevalence.R’
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• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from:   ‘RcppParallel’ ‘rstantools’   All declared Imports should be used.
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• checking compiled code ... OK
• checking examples ... [11s/12s] ERROR Running examples in ‘PoolTestR-Ex.R’ failed The error most likely occurred in: > ### Name: PoolRegBayes > ### Title: Bayesian Mixed or Fixed Effect Logistic Regression with > ### Presence/Absence Tests on Pooled Samples > ### Aliases: PoolRegBayes > > ### ** Examples > > # Perform logistic-type regression modelling for a synthetic dataset consisting > # of pools (sizes 1, 5, or 10) taken from 4 different regions and 3 different > # years. Within each region specimens are collected at 4 different villages, > # and within each village specimens are collected at 8 different sites. > > > ### Models in a frequentist framework > #ignoring hierarchical sampling frame within each region > Mod <- PoolReg(Result ~ Region + Year, + data = SimpleExampleData, + poolSize = NumInPool) [1] "Model has no group/random effects. Using a fixed effect model (glm)" > summary(Mod) Call: stats::glm(formula = formula, family = stats::binomial(PoolLink(data[[poolSize]])),     data = data) Coefficients:             Estimate Std. Error z value Pr(>|z|) (Intercept) -1.97190 0.12559 -15.701 < 2e-16 *** RegionB -1.20591 0.17890 -6.741 1.58e-11 *** RegionC -2.40943 0.27082 -8.897 < 2e-16 *** RegionD -0.11001 0.14466 -0.760 0.4470 Year -0.13874 0.07716 -1.798 0.0722 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for binomial family taken to be 1)     Null deviance: 1304.34 on 1151 degrees of freedom Residual deviance: 990.58 on 1147 degrees of freedom AIC: 1000.6 Number of Fisher Scoring iterations: 6 > > #accounting hierarchical sampling frame within each region > HierMod <- PoolReg(Result ~ Region + Year + (1|Village) + (1|Site), + data = SimpleExampleData, + poolSize = NumInPool) [1] "Detected group/random effects. Using a mixed effect model (glmer)" Error: Downdated VtV is not positive definite Execution halted
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• checking for non-standard things in the check directory ... OK
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• DONE

Status: 1 ERROR, 2 NOTEs